Replace deprecated pr.create_job in first_steps.ipynb

[samwaseda]

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[samwaseda]

To be honest it's a horrible idea to show an example to heat up Aluminium to 1,000 K...

[pkruzikova]

Looks good to me. I am assuming the replacing pr.create for structures will be done elsewhere (if planned) as it is not in the PL title, and it's good to see the warnings about it now.

[niklassiemer]

Since we are testing this from the pyiron repo, I would stick to from pyiron import Project

[samwaseda]

Hmmm I see your point, but pyiron takes so much more time that it might be a bit discouraging to see this in the very first line

[niklassiemer]

Yes, but this is the only test-space to check that the from pyiron import is working correctly! Maybe we have to make the lookup faster if it is just too annoying? Or is it because you also have all the other pyiron modules installed which are not loaded in a nice way (especially contrib...). I mean if only

conda create --name pyiron pyiron

was used it should essentially only find and load pyiton_atomistics at a moderate overhead?

[samwaseda]

Yes, but this is the only test-space to check that the from pyiron import is working correctly!

Would your concern be addressed if I create an example notebook that uses e.g. both pyiron_atomistics and pyiron_continuum?

[liamhuber]

No, I'm with Niklas here -- this is basically the only place that we might reasonably from pyiron import... and then expect that to be providing us with sub module support (atomistics, continuum, etc). So if that's something we want to provide, IMO this is the right place to test it. The fact it's painfully slow is related, but a separate issue.

[niklassiemer]

I am in favor of leaving it from pyiron here. However, it might be reasonable to use the notebooks from the pyiron_atomistics repo for the education on the website.
Furthermore, we probably should raise an issue for the slow import.
Some solution could be:

• not import but only find other pyiron_modules than pyiron_atomistics on import of pyiron and import those upon access.
• provide a module scoped list (dict? ) which is used to omit the finding in the first place, i.e. a list like ['contrib', 'gui', ... ] which is used for autocompletion and to extend this to the corresponding pyiron_module. If a not listed access pyiron.some_mod is performed try to import pyiron_some_mod and use this.
• stop treating pyiron as drop in replacement of pyiron_atomistics and actually use pyiron.atomistics (probably together with one of the first). Breaks backwards compatibility, though!

[samwaseda]

I am in favor of leaving it from pyiron here. However, it might be reasonable to use the notebooks from the pyiron_atomistics repo for the education on the website.

ok that means I should copy this notebook to pyiron_atomistics and create an integration tests folder where we'd have essentially the same content with from pyiron import Project?

[niklassiemer]

I did not check the exact content, but aren't the notebooks here exactly such copies from pyiron_atomistics with the from pyiron to from pyiron_atomistics change? It is a not so nice setup, since near duplication, i.e. please apply the same changes over in pyiron_atomistics 😇

[niklassiemer]

And I really meant for the purpose of displaying on the webpage. Right now, the tutorial is from this repo, while you claim it to be much faster if we use the notebooks from pyiron_atomistics for the webpage.

[samwaseda]

I did not check the exact content, but aren't the notebooks here exactly such copies from pyiron_atomistics with the from pyiron to from pyiron_atomistics change?

AHA!! I didn't know that it existed TWICE!

And I really meant for the purpose of displaying on the webpage.

I'm not really sure if I understand what you are referring to. Do I understand it correctly:

• We keep from pyiron import Project in this repo
• On the website we use the version from pyiron_atomistics, i.e. the same notebook with from pyiron_atomistics import Project?

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